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Genome-wide identification and analysis of basic helix-loop-helix domains in dog, Canis lupus familiaris

MOLECULAR GENETICS AND GENOMICS 2015年第2期290卷 633-648页

作者： Wang, Xu-Hua Wang, Yong Liu, A-Ke Liu, Xiao-Ting Zhou, Yang Yao, Qin Chen, Ke-Ping Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China Jiangsu Univ Sch Food & Biol Engn Zhenjiang 212013 Peoples R China

The basic helix-loop-helix (bHLH) domain is a highly conserved amino acid motif that defines a group of DNA-binding transcription factors. bHLH proteins play essential regulatory roles in a variety of biological processes in animal, plant, and fungus. The domestic dog, Canis lupus familiaris, is a good model organism for genetic, physiological, and behavioral studies. In this study, we identified 115 putative bHLH genes in the dog genome. Based on a phylogenetic analysis, 51, 26, 14, 4, 12, and 4 dog bHLH genes were assigned to six separate groups (A-F);four bHLH genes were categorized as ''orphans''. Within-group evolutionary relationships inferred from the phylogenetic analysis were consistent with positional conservation, other conserved domains flanking the bHLH motif, and highly conserved intron/exon patterns in other vertebrates. Our analytical results confirmed the GenBank annotations of 89 dog bHLH proteins and provided information that could be used to update the annotations of the remaining 26 dog bHLH proteins. These data will provide good references for further studies on the structures and regulatory functions of bHLH proteins in the growth and development of dogs, which may help in understanding the mechanisms that underlie the physical and behavioral differences between dogs and wolves.

关键词： basic helix-loop-helix Canis lupus familiaris Phylogenetic analysis BLAST search Ortholog

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A Genome-Wide Identification of basic helix-loop-helix Motifs in Pediculus humanus corporis (Phthiraptera: Pediculidae)

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JOURNAL OF INSECT SCIENCE 2014年第195期14卷 1-10页

作者： Wang, Xu-Hua Wang, Yong Zhang, De-Bao Liu, A-Ke Yao, Qin Chen, Ke-Ping Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China Jiangsu Univ Sch Food & Biol Engn Zhenjiang 212013 Peoples R China

basic helix-loop-helix (bHLH) proteins comprise a large superfamily of transcription factors, which are involved in the regulation of various developmental processes. bHLH family members are widely distributed in various eukaryotes including yeast, fruit fly, zebrafish, mouse, and human. In this study, we identified 55 bHLH motifs encoded in genome sequence of the human body louse, Pediculus humanus corporis (Phthiraptera: Pediculidae). Phylogenetic analyses of the identified P. humanus corporis bHLH (PhcbHLH) motifs revealed that there are 23, 11, 9, 1, 10, and 1 member(s) in groups A, B, C, D, E, and F, respectively. Examination to GenBank annotations of the 55 PhcbHLH members indicated that 29 PhcbHLH proteins were annotated in consistence with our analytical result, 8 were annotated different with our analytical result, 12 were merely annotated as hypothetical protein, and the rest 6 were not deposited in GenBank. A comparison on insect bHLH gene composition revealed that human body louse possibly has more hairy and E(spl) genes than other insect species. Because hairy and E(spl) genes have been found to negatively regulate the differentiation of insect preneural cells, it is suggested that the existence of additional hairy and E(spl) genes in human body louse is probably the consequence of its long period adaptation to the relatively dark and stable environment. These data provide good references for further studies on regulatory functions of bHLH proteins in the growth and development of human body louse.

关键词： basic helix-loop-helix phylogenetic analysis ortholog Pediculus humanus corporis BLASTsearch

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Possible roles of basic helix-loop-helix transcription factors in adaptation to drought

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PLANT SCIENCE 2014年 223卷 1-7页

作者： Castilhos, Graciela Lazzarotto, Fernanda Spagnolo-Fonini, Leila Bodanese-Zanettini, Maria Helena Margis-Pinheiro, Marcia Univ Fed Rio Grande do Sul Dept Genet Programa Posgrad Genet & Biol Mol BR-91501970 Porto Alegre RS Brazil Univ Fed Rio Grande do Sul Programa Posgrad Biol Celular & Mol BR-91501970 Porto Alegre RS Brazil

Water deficiency decreases plant growth and productivity. Several mechanisms are activated in response to dehydration that allows plants to cope with stress, including factors controlling stomatal aperture and ramified root system development. In addition, ABA metabolism is also implicated in the regulation of drought responses. The basic helix-loop-helix (bHLH) proteins, a large family of conserved transcription factors that regulates many cellular processes in eukaryotic organisms, are also involved in several responses that are important for plants to cope with drought stress. This review discusses distinct mechanisms related to drought-adaptive responses, especially the possible involvement of the bHLH transcription factors such as MUTE, implicated in stomatal development;RD29, an ABA-responsive gene;EGL3 and GL3, involved in thichome and root hair development;and SPT, which play roles in repressing leaf expansion. Transcription factors are potential targets for new strategies to increase the tolerance of cultivars to drought stress. Recognition of gene regulatory networks in crops is challenging, and the manipulation of bHLH genes as well as components that mediate bHLH transcription factor responses in different pathways could be essential to achieve abiotic stress tolerance in plants through genetic manipulation. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

关键词： basic helix-loop-helix Drought stress Stomata Root hair Trichome Transcription factor

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Genome-wide characterization of the bHLH gene family in Gynostemma pentaphyllum reveals its potential role in the regulation of gypenoside biosynthesis

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BMC PLANT BIOLOGY 2024年第1期24卷 205页

作者： Qin, Yanhong Li, Jinmei Chen, Jianhua Yao, Shaochang Li, Liangbo Huang, Rongshao Tan, Yong Ming, Ruhong Huang, Ding Guangxi Univ Chinese Med Coll Pharm Nanning 530200 Peoples R China Guangxi Univ Chinese Med Guangxi Key Lab Zhuang & Yao Ethn Med Nanning 530200 Peoples R China

Background Gynostemma pentaphyllum, an ancient Chinese herbal medicine, serves as a natural source of gypenosides with significant medicinal properties. basic helix-loop-helix (bHLH) transcription factors play pivotal roles in numerous biological processes, especially in the regulation of secondary metabolism in plants. However, the characteristics and functions of the bHLH genes in G. pentaphyllum remain unexplored, and their regulatory role in gypenoside biosynthesis remains poorly elucidated. Results This study identified a total of 111 bHLH members in G. pentaphyllum (GpbHLHs), categorizing them into 26 subgroups based on shared conserved motif compositions and gene structures. Collinearity analysis illustrated that segmental duplications predominately lead to the evolution of GpbHLHs, with most duplicated GpbHLH gene pairs undergoing purifying selection. Among the nine gypenoside-related GpbHLH genes, two GpbHLHs (GpbHLH15 and GpbHLH58) were selected for further investigation based on co-expression analysis and functional prediction. The expression of these two selected GpbHLHs was dramatically induced by methyl jasmonate, and their nuclear localization was confirmed. Furthermore, yeast one-hybrid and dual-luciferase assays demonstrated that GpbHLH15 and GpbHLH58 could bind to the promoters of the gypenoside biosynthesis pathway genes, such as GpFPS1, GpSS1, and GpOSC1, and activate their promoter activity to varying degrees. Conclusions In conclusion, our findings provide a detailed analysis of the bHLH family and valuable insights into the potential use of GpbHLHs to enhance the accumulation of gypenosides in G. pentaphyllum.

关键词： Gynostemma pentaphyllum basic helix-loop-helix Genome-wide characterization Transcription factor Gypenoside biosynthesis

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The arabidopsis bHLH transcription factor family

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TRENDS IN PLANT SCIENCE 2024年第6期29卷 668-680页

作者： Gao, Fei Dubos, Christian Hunan Agr Univ Coll Agron Changsha 410128 Peoples R China Yuelushan Lab Changsha 410128 Peoples R China Univ Montpellier Inst Agro IPSiM CNRSINRAE Montpellier France

basic helix-loop-helices (bHLHs) are present in all eukaryotes and form one of the largest families of transcription factors (TFs) found in plants. bHLHs function as transcriptional activators and/or repressors of genes involved in key processes involved in plant growth and development in interaction with the environment (e.g., stomata and root hair development, iron homeostasis, and response to heat and shade). Recent studies have improved our understanding of the functioning of bHLH TFs in complex regulatory networks where a series of post-translational modifications (PTMs) have critical roles in regulating their stability (e.g., protein-protein interactions, phosphorylation, ubiquitination, and sumoylation). Further elucidating the function and regulation of bHLHs will help further understanding of the biology of plants in general and for the development of new tools for crop improvement.

关键词： basic helix-loop-helix heat iron root hair shade stomata

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Phylogenetic analyses of vector mosquito basic helix-loop-helix transcription factors

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INSECT MOLECULAR BIOLOGY 2013年第5期22卷 608-621页

作者： Zhang, D. B. Wang, Y. Liu, A. K. Wang, X. H. Dang, C. W. Yao, Q. Chen, K. P. Jiangsu Univ Inst Life Sci Zhenjiang 212013 Peoples R China Jiangsu Univ Sch Food & Biol Engn Zhenjiang 212013 Peoples R China Binxian High Sch Xianyang Peoples R China

basic helix-loop-helix (bHLH) transcription factors play critical roles in the regulation of a wide range of developmental processes in higher organisms and have been identified in more than 20 organisms. Mosquitoes are important vectors of certain human diseases. In this study, Aedes aegypti, Anopheles gambiae str. PEST and Culex quinquefasciatus genomes were found to encode 55, 55 and 57 bHLH genes, respectively. Further phylogenetic analyses and OrthoDB and Kyoto encyclopedia of genes and genomes orthology database searches led us to define orthology for all the identified mosquito bHLHs successfully. This provides useful information with which to update annotations to 40 ***, 55 *** and 38 *** genes in VectorBase. The mosquito lineage has more bHLH genes in the Atonal, neurogenin (Ngn) and Hes-related with YRPW motif (Hey) families than do other insect species, suggesting that mosquitoes have evolved to be more sensitive to vibration, light and chemicals. Mosquito bHLH genes generally have higher evolutionary rates than other insect species. However, no pervasive positive selection occurred in the evolution of insect bHLH genes. Only episodic positive selection was found to affect evolution of bHLH genes in 11 families. Besides, coding regions of several *** motifs have unusually long introns in which multiple copies of transposable elements have been identified. These data provide a solid basis for further studies on structures and functions of bHLH proteins in the regulation of mosquito development and for prevention and control of mosquito-mediated human diseases.

关键词： basic helix-loop-helix transcription factor vector mosquito phylogenetic analysis

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Identification of bHLH transcription factors and screening of anthocyanin-related genes in Lagerstroemia indica

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GENETICA 2024年第4-6期152卷 179-197页

作者： Yu, Mengxin Bai, Mingzhu Chen, Mengmeng Zhang, Guozhe Zhao, Yu Ma, Qingqing Yang, Liyuan Gu, Cuihua Zhejiang A&F Univ Coll Landscape Architecture Hangzhou 311300 Peoples R China Zhejiang A&F Univ Zhejiang Prov Key Lab Germplasm Innovat & Utilizat Hangzhou 311300 Peoples R China Zhejiang A&F Univ Key Lab Natl Forestry & Grassland Adm Germplasm In Hangzhou 311300 Peoples R China

The basic helix-loop-helix (bHLH) family is one of the three major transcription factor families that play important transcriptional regulatory roles in plant growth and development. One of the most crucial elements in defining Lagerstroemia indica's decorative qualities is flower color. However, the function of the bHLH transcription factor family in L. indica anthocyanin glycoside synthesis has not been clarified. Using the transcriptome data of flower color, 79 LibHLH genes were found in this study. Phylogenetic analysis showed that the LibHLH genes can be divided into 16 subfamilies, and most of the genes in the same subfamily have similar conserved motifs. The total anthocyanin glycoside content of L. indica 'Zihua Guifei' petals was determined during three developmental stages of the petals' growth. The results showed that the total anthocyanin glycoside content grew gradually with growth and development, and that it accumulated most during the full bloom stage. By using gene expression analysis, protein interaction network analysis, and bioinformatics, it was possible to determine which member of the III f family, LibHLH29, is important for the synthesis of anthocyanin glycosides in L. indica. Its expression was confirmed by qRT-PCR, and the results were essentially compatible with the transcriptome data. It was more prominent in the light-colored bloom stage the color-transition stage of L. indica 'Zihua Guifei'. It can be further investigated as a major candidate gene for regulating anthocyanin glycoside synthesis in L. indica, thus laying the foundation for an in-depth study of the interactions among transcription factors.

关键词： Lagerstroemia indica basic helix-loop-helix Phylogeny Gene expression Anthocyanin

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The basic helix-loop-helix transcription factor Hand1 regulates mouse development as a homodimer

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DEVELOPMENTAL BIOLOGY 2013年第2期382卷 470-481页

作者： Hu, Dong Scott, Ian C. Snider, Fran Geary-Joo, Colleen Zhao, Xiang Simmons, David G. Cross, James C. Univ Calgary Fac Med Dept Biochem & Mol Biol Calgary AB Canada Univ Calgary Fac Vet Med Dept Comparat Biol & Expt Med Calgary AB Canada Huazhong Univ Sci & Technol Tongji Med Coll Union Hosp Ctr Stem Cell Applicat & Res Wuhan 430074 Peoples R China Hosp Sick Children Toronto ON M5G 1X5 Canada Univ Queensland Sch Biomed Sci Bne Qld 4072 Australia

Hand1 is a basic helix-loop-helix transcription factor that is essential for development of the placenta, yolk sac and heart during mouse development. While Hand1 is essential for trophoblast giant cell (TGC) differentiation, its potential heterodimer partners are not co-expressed in TGCs. To test the hypothesis that Hand1 functions as homodimer, we generated knock-in mice in which the Hand1 gene was altered to encode a tethered homodimer (TM). Some Hand 1m/- conceptuses in which the only form of Hand1 is Hand1 TH are viable and fertile, indicating that homodimer Hand1 is sufficient for mouse survival. --2/3 of Hand1mi- and all Hand1THMI mice died in utero and displayed severe placental defects and variable cardial and cranial-facial abnormalities, indicating a dosage-dependent effect of Hand1m Meanwhile, expression of the Hand1TH protein did not have negative effects on viability or fertility in all Hand1mh mice. These data imply that Hand1 homodimer plays a dominant role during development and its expression dosage is critical for survival, whereas Hand1 heterodimers can be either dispensable or play a regulatory role to modulate the activity of Hand1 homodimer in vivo. 0 2013 Elsevier Inc. All rights reserved.

关键词： Hand1 basic helix-loop-helix Transcription factor Homodimer Mouse development Trophoblast

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Phylogenetic analysis of bHLH classes III and IV in land plants and their algal relatives

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NEW PHYTOLOGIST 2023年第5期240卷 1717-1721页

作者： Kongsted, Thea E. E. Glover, Beverley J. J. Univ Cambridge Dept Plant Sci Downing St Cambridge CB2 3EA England

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Dependence on clade II bHLH transcription factors for nursing of haploid products by tapetal-like cells is conserved between moss sporangia and angiosperm anthers

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NEW PHYTOLOGIST 2022年第2期235卷 718-731页

作者： Lopez-Obando, Mauricio Landberg, Katarina Sundberg, Eva Thelander, Mattias Swedish Univ Agr Sci Linnean Ctr Plant Biol Uppsala Dept Plant Biol POB 7080 SE-75007 Uppsala Sweden VEDAS Corp Invest & Innovac VEDASCII Cl 8 B 65-261 Medellin 050024 Colombia

Clade II basic helix-loop-helix transcription factors (bHLH TFs) are essential for pollen production and tapetal nursing functions in angiosperm anthers. As pollen has been suggested to be related to bryophyte spores by descent, we characterized two Physcomitrium (Physcomitrella) patens clade II bHLH TFs (PpbHLH092 and PpbHLH098), to test if regulation of sporogenous cells and the nursing cells surrounding them is conserved between angiosperm anthers and bryophyte sporangia. We made CRISPR-Cas9 reporter and loss-of-function lines to address the function of PpbHLH092/098. We sectioned and analyzed WT and mutant sporophytes for a comprehensive stage-by-stage comparison of sporangium development. Spore precursors in the P. patens sporangium are surrounded by nursing cells showing striking similarities to tapetal cells in angiosperms. Moss clade II bHLH TFs are essential for the differentiation of these tapetal-like cells and for the production of functional spores. Clade II bHLH TFs provide a conserved role in controlling the sporophytic somatic cells surrounding and nursing the sporogenous cells in both moss sporangia and angiosperm anthers. This supports the hypothesis that such nursing functions in mosses and angiosperms, lineages separated by roughly 450 million years, are related by descent.

关键词： basic helix-loop-helix bryophytes moss Physcomitrium patens sporangium sporogenesis tapetum transcription factor

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